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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcctgtttccaccaaatagaattcgttattaagctgatgtagtctttattttctatttggccaagtgctaatatttttgtgttgcctgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTGTAAGTGCCATTGTCTTCTAATG

Basic information

species Zea mays
transcript GRMZM2G152775_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G152775_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 3'ss of exon 1
ctcctgtttccaccaaatagaattcgttattaagctgatgtagtcttta---ttttctatttggcca----agtgctaatatttttgtgttgcc-tgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTGTAAGTGCCATTGTCTTCTAATG
        |  | | ||| ||| ||  ||||||| || |||  ||| |    || |||||||   |     | |   | |   |||||  ||   || |    || |||||||||||| || |||||||| || ||||| |||||||||||||| ||||||||||| ||||| ||||||||||||                       
--------ttgatccaatcgaaatcaatattaagttggtgtgctctgtctgcttgtctattttttccctttaatttaattgcctttgttatgtggtgttaattcttagGAATGTATGTGGCGAACCGTGCATCTGACAAAATTACTCAACTGACTGACAATGTGTACGTCTGCCGCTCTGGATCT-----------------------

upper sequence: GRMZM2G152775_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g53060.2 (Oryza sativa), 3'ss of exon 1
ctcctgtttccaccaaatagaattcgttattaagctgatgtagtct-ttattttctatttggccaagtgctaatat-ttttgtgttgcctgctccaa---ctcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTGTAAGTGCCATTGTCTTCTAATG
    ||||   | | ||  ||| ||| | ||| | ||| ||| | | ||  ||| | ||   |       ||||||    | ||||| ||| |   |   || |||||||||||| || |||||||| || |||||||||||||| || || |||||||||||  |||| ||||||||||||                       
---atgttctgaaccaactgaaatcgatgttatgttgacgtactatgttggtttttgtt--actttcctttaatataccctttgttgtctggtattaattcttagGAATGTATGTGGCAAACCGTGCGTCGGACAAGATTACTCAGCTAACTGACAATGTGTACATCTGCCGCTCTGGATCT-----------------------

upper sequence: GRMZM2G152775_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT4G31300.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------------------ctcctgtttccacca-aatagaattcgttattaagctgatgtagtctttattttctatttggccaagtgctaatatttt--tgtgttgcctgct-ccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTGTAAGTGCCATTGTCTTCTAATG
                                                                        |   ||||| | |  || | |      |  ||| |   |||  | |||   |  | |   |  |  || |||  ||    | |||||     | |   | |||| ||||| ||||| || || ||||| || |||||||| ||||||||||| ||||| || ||||| |||||||||||                        
gtgagatttccccccttctctacttttctagggttttagttcctcttcgttgggtttgtatttgagttttgttttcgtttcaatcggaacaaagaataatcctaatcgattgttctatttgggtaatttagagaaagctgttaaatttgggatctgttgtaaattactcgcgcagGTATGTACGTAGCGAATCGAGCTTCTGATAAGATTACACAACTGACAGATAATGTCTACGTCTGCCGCTCTGGATCG-----------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|211419582|gb|FK988615.1|FK988615
EST:     CTGCTACGAGGGCGGCGTCGTCCTNGGCTCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
EST: gi|161589696|gb|EY963443.1|EY963443
EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGTCTTCA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTG-CTTCA
EST: gi|76014048|gb|DT941218.1|DT941218
EST:     CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA
genomic: CTGCTACGAGGGCGGCGTCGTCCTGGGCGCCGATTCCAGGACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttctatttggccaagtgctaatatttttgtgttgcctgctccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACTCAACTGACAGACAATGTGTATGTCTGTCGCTCTGGATCTGTAAGTGCCATTGTCTTCTAATG
                     tgctaat  putative branch site (score: 2)
                                        cctgctcc  putative PPT
                        taatatttttgtgtt  TA-rich tract